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IntaRNA 6571257

Input and runtime details for job 6571257 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Index first query position1
? Target RNA (long) in FASTA[.fa]
? Target NCBI RefSeq IDNC_000913
? All repliconsyes
? Extract sequences aroundstart codon
? nt upstream (1-300)75
? nt downstream (1-300)75
? Index first target position-75

Output Parameters

? Number of interactions per RNA pair1
? Suboptimal interaction overlap can overlap in query
? Max. interaction lengthnot provided
? Max. absolute energy of an interaction0
? Max. delta energy above mfe of an interaction100
? No lonely base pairsyes
? No GU at helix endsyes

Seed Parameters

? Min. number of basepairs in seed7
? Max. Number of mismatches in seed0
? Maximal energy0
? Minimal unpaired probability (per RNA)0
? Seed position (query)not provided
? Seed position (target)not provided
? Ignore seeds with GU base pairsno
? Ignore seeds with GU endsyes

Folding Parameters

? Temperature for energy computation37.0
? Access. query: folding window size150
? Access. query: max. basepair distance100
? Access. target: folding window size150
? Access. target: max. basepair distance100
? Energy parameter set (Vienna package) Turner model, 2004

Job ID 6571257 (server version trunk)

?Job Submitted & Queued@ Mon Jan 27 14:18:03 CET 2020
?Processing Started@ Mon Jan 27 14:20:22 CET 2020
?IntaRNA Finished & Post-Processing@ Mon Jan 27 14:21:19 CET 2020
?Post-Processing Finished@ Mon Jan 27 14:22:25 CET 2020
?Job Completed@ Mon Jan 27 14:22:35 CET 2020
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=6571257&toolName=IntaRNA ( 30 days expiry )

The job description you specified

Spot42 - E. coli


? Output download complete results [zip]

Downloadable files

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heatmap

? Identified Interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Sort by selecting a column name
Target Start(T) End(T) Query Start(Q) End(Q) Energy p-value fdr gene annotation
b3503 -75 -69 Spot42 1 7 -9.14 0.0246155 0.9238006 arsC arsenate reductase
b0646 -74 -67 Spot42 1 8 -10.27 0.0129952 0.9238006 djlB putative HscC co-chaperone uncharacterized J domain-containing protein
b3921 -74 -67 Spot42 50 57 -9.55 0.0195371 0.9238006 yiiR DUF805 family putative inner membrane protein
b2294 -75 -67 Spot42 48 56 -8.74 0.0308106 0.9238006 yfbU UPF0304 family protein
b0367 -75 -66 Spot42 52 61 -10.23 0.0132937 0.9238006 tauC taurine ABC transporter permease
b4174 -75 -61 Spot42 42 57 -9.36 0.0217476 0.9238006 hflK modulator for HflB protease specific for phage lambda cII repressor
b2602 -71 -60 Spot42 7 18 -10.62 0.0106505 0.9238006 yfiL lipoprotein
b1004 -75 -56 Spot42 10 32 -9.83 0.0166769 0.9238006 wrbA NAD(P)H:quinone oxidoreductase
b2797 -68 -54 Spot42 55 69 -15.99 0.0004824 0.8439588 sdaB L-serine dehydratase 2
b1106 -58 -52 Spot42 1 7 -10.06 0.0146397 0.9238006 thiK thiamine kinase
b1623 -58 -51 Spot42 1 8 -9.03 0.0261856 0.9238006 add adenosine deaminase
b3224 -61 -50 Spot42 1 12 -16.33 0.0003958 0.8439588 nanT sialic acid transporter
b2216 -57 -49 Spot42 3 11 -10.78 0.009723 0.9238006 rcsD phosphotransfer intermediate protein in two-component regulatory system with RcsBC
b0369 -53 -46 Spot42 1 8 -8.81 0.0296259 0.9238006 hemB 5-aminolevulinate dehydratase (porphobilinogen synthase)
b0721 -55 -44 Spot42 4 15 -10.51 0.0113383 0.9238006 sdhC succinate dehydrogenase membrane subunit binds cytochrome b556
b3934 -56 -44 Spot42 41 56 -10.45 0.0117318 0.9238006 cytR Anti-activator for CytR-CRP nucleoside utilization regulon
b0882 -74 -44 Spot42 3 32 -9.02 0.0263331 0.9238006 clpA ATPase and specificity subunit of ClpA-ClpP ATP-dependent serine protease chaperone activity
b4553 -64 -42 Spot42 53 74 -11.45 0.006633 0.9238006 ysaB uncharacterized protein
b3709 -53 -42 Spot42 1 13 -9.62 0.0187797 0.9238006 tnaB tryptophan transporter of low affinity
b4621 -48 -41 Spot42 1 8 -11.15 0.0078733 0.9238006 yjbS uncharacterized protein
b3816 -71 -41 Spot42 4 37 -10.38 0.012208 0.9238006 corA magnesium/nickel/cobalt transporter
b0523 -51 -41 Spot42 3 13 -8.91 0.0280104 0.9238006 purE N5-carboxyaminoimidazole ribonucleotide mutase
b1927 -50 -39 Spot42 48 59 -13.13 0.0025285 0.9238006 amyA cytoplasmic alpha-amylase
b2506 -51 -37 Spot42 55 68 -11.81 0.0053979 0.9238006 yfgI nalidixic acid resistance protein putative periplasmic protein
b3685 -51 -36 Spot42 54 68 -11.08 0.0081942 0.9238006 yidE putative transporter
b0835 -52 -36 Spot42 1 13 -10 0.0151462 0.9238006 rimO ribosomal protein S12 methylthiotransferase
b1347 -46 -34 Spot42 20 32 -10.44 0.0117987 0.9238006 ydaC DUF1187 family protein Rac prophage putative double-strand break reduction protein
b1792 -68 -32 Spot42 40 73 -9.23 0.0234 0.9238006 yeaO DUF488 family protein
b1901 -37 -30 Spot42 1 8 -11.04 0.0083834 0.9238006 araF L-arabinose ABC transporter periplasmic binding protein
b2801 -39 -29 Spot42 46 56 -12.84 0.002988 0.9238006 fucP L-fucose transporter
b2221 -36 -27 Spot42 1 11 -10.63 0.01059 0.9238006 atoD acetyl-CoA:acetoacetyl-CoA transferase alpha subunit
b0333 -32 -26 Spot42 1 7 -10 0.0151462 0.9238006 prpC 2-methylcitrate synthase
b2659 -45 -24 Spot42 1 24 -10.83 0.0094499 0.9238006 csiD carbon starvation protein
b4361 -33 -23 Spot42 55 65 -9.75 0.0174491 0.9238006 dnaC DNA biosynthesis protein
b2150 -48 -22 Spot42 1 24 -9.49 0.0202101 0.9238006 mglB methyl-galactoside transporter subunit
b2715 -28 -21 Spot42 1 8 -9.51 0.0199833 0.9238006 ascF cellobiose/arbutin/salicin-specific PTS enzymes IIB and IC components
b3078 -27 -20 Spot42 1 8 -10.33 0.0125598 0.9238006 ygjI putative transporter
b2357 -27 -17 Spot42 55 65 -10.32 0.0126314 0.9238006 yfdN CPS-53 (KpLE1) prophage uncharacterized protein
b4311 -27 -16 Spot42 1 12 -11.59 0.0061225 0.9238006 nanC N-acetylnuraminic acid outer membrane channel protein
b2407 -22 -16 Spot42 1 7 -8.77 0.0302973 0.9238006 xapA purine nucleoside phosphorylase 2 nicotinamide 1-beta-D-riboside synthase
b0969 -24 -15 Spot42 50 59 -9.29 0.0226226 0.9238006 tusE mnm(5)-s(2)U34-tRNA 2-thiolation sulfurtransferase
b1300 -28 -13 Spot42 44 58 -9.81 0.0168668 0.9238006 puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase succinate semialdehyde dehydrogenase
b2548 -17 -11 Spot42 1 7 -9.25 0.023138 0.9238006 yphF putative sugar ABC transporter periplasmic binding protein
b0885 -27 -10 Spot42 42 58 -13.52 0.0020193 0.9238006 aat leucyl/phenylalanyl-tRNA-protein transferase
b0728 -20 -9 Spot42 23 34 -9.01 0.0264814 0.9238006 sucC succinyl-CoA synthetase beta subunit
b0347 -21 -6 Spot42 41 57 -8.74 0.0308106 0.9238006 mhpA 3-(3-hydroxyphenyl)propionate hydroxylase
b3238 -21 -5 Spot42 39 54 -9.61 0.0188861 0.9238006 yhcN cadmium and peroxide resistance protein stress-induced
b1398 -10 -2 Spot42 1 9 -13.17 0.0024709 0.9238006 paaK phenylacetyl-CoA ligase
b1751 -14 -2 Spot42 21 33 -9.65 0.0184641 0.9238006 ydjY putative ferrodoxin-like lipoprotein
b4465 -18 -2 Spot42 39 56 -8.82 0.0294603 0.9238006 yggP putative Zn-binding dehydrogenase
b1553 -15 -1 Spot42 20 34 -9.05 0.025893 0.9238006 rzpQ Rz-like protein Qin prophage
b1302 -35 6 Spot42 21 57 -11.97 0.004925 0.9238006 puuE 4-aminobutyrate aminotransferase PLP-dependent
b0511 -28 10 Spot42 18 58 -9.6 0.0189931 0.9238006 ybbW putative allantoin transporter
b3690 -4 11 Spot42 17 31 -9.42 0.0210242 0.9238006 cbrA colicin M resistance protein FAD-binding protein putative oxidoreductase
b0246 8 14 Spot42 1 7 -8.71 0.0313324 0.9238006 yafW CP4-6 prophage antitoxin of the YkfI-YafW toxin-antitoxin system
b2980 2 16 Spot42 18 33 -10.39 0.0121389 0.9238006 glcC glycolate-inducible glc operon transcriptional repressor autorepressor
b2561 -7 16 Spot42 11 32 -10.17 0.0137542 0.9238006 yfhH putative DNA-binding transcriptional regulator
b3908 -12 16 Spot42 1 34 -9.96 0.0154934 0.9238006 sodA superoxide dismutase Mn
b3683 5 16 Spot42 55 66 -9.25 0.023138 0.9238006 glvC pseudogene arbutin specific enzyme IIC component of PTSenzyme Transport of small molecules: Carbohydrates organic acids alcohols PTS system arbutin-like IIB component PTS system arbutin-like IIC component
b3139 13 19 Spot42 1 7 -9.42 0.0210242 0.9238006 agaC N-acetylgalactosamine-specific enzyme IIC component of PTS
b2319 3 19 Spot42 20 36 -9.12 0.0248939 0.9238006 usg putative semialdehyde dehydrogenase
b2582 6 19 Spot42 4 16 -9.03 0.0261856 0.9238006 trxC thioredoxin 2
b1862 13 20 Spot42 1 8 -9.04 0.0260389 0.9238006 yebB DUF830 family protein
b1586 -1 24 Spot42 5 28 -9.23 0.0234 0.9238006 ynfD DUF1161 family periplasmic protein
b3311 17 25 Spot42 1 9 -9.59 0.0191007 0.9238006 rpsQ 30S ribosomal subunit protein S17
b1212 15 28 Spot42 43 56 -13.07 0.0026174 0.9238006 prmC RF-1 and RF-2 N5-glutamine methyltransferase
b3051 19 28 Spot42 3 12 -10.36 0.0123476 0.9238006 yqiK PHB family membrane protein function unknown
b0774 9 28 Spot42 4 24 -9.09 0.0253174 0.9238006 bioA 78-diaminopelargonic acid synthase PLP-dependent
b3664 17 32 Spot42 40 56 -10.58 0.0108957 0.9238006 adeQ adenine permease high affinity adenine:H+ symporter
b4659 25 32 Spot42 49 56 -8.71 0.0313324 0.9238006 yabP pseudogene pentapeptide repeats-containing
b0718 20 33 Spot42 1 14 -10.35 0.0124179 0.9238006 ybgQ putative outer membrane protein
b1343 21 34 Spot42 11 24 -8.89 0.0283265 0.9238006 dbpA ATP-dependent RNA helicase specific for 23S rRNA
b1385 21 37 Spot42 55 71 -11.57 0.006193 0.9238006 feaB phenylacetaldehyde dehydrogenase
b3465 27 38 Spot42 54 65 -8.75 0.0306386 0.9238006 rsmD 16S rRNA m(2)G966 methyltransferase SAM-dependent
b0757 -17 39 Spot42 1 59 -14.73 0.001003 0.9238006 galK galactokinase
b0705 41 48 Spot42 49 56 -9.4 0.0212627 0.9238006 ybfL pseudogene DDE domain transposase familyputative factor Not classified putative receptor protein
b0954 28 49 Spot42 9 31 -9.87 0.0163036 0.9238006 fabA beta-hydroxydecanoyl thioester dehydrase
b0559 38 49 Spot42 46 58 -9.04 0.0260389 0.9238006 ybcW DLP12 prophage uncharacterized protein
b2467 55 61 Spot42 1 7 -9.96 0.0154934 0.9238006 nudK GDP-mannose pyrophosphatase
b1695 43 63 Spot42 48 71 -8.85 0.028969 0.9238006 ydiO putative acyl-CoA dehydrogenase
b1391 56 67 Spot42 55 66 -10.65 0.0104701 0.9238006 paaD ring 12-phenylacetyl-CoA epoxidase subunit
b3878 60 67 Spot42 1 8 -10.22 0.0133694 0.9238006 yihQ putative sulpholipid alpha-glucosidase alpha-glucosyl fluoride glucosidase
b2962 26 68 Spot42 4 57 -10.78 0.009723 0.9238006 yggX oxidative damage protective factor for iron-sulfur proteins
b3827 60 68 Spot42 1 9 -9.16 0.0243401 0.9238006 yigM putative inner membrane EamA-like transporter
b3092 6 69 Spot42 1 57 -10.14 0.0139903 0.9238006 uxaC uronate isomerase
b1487 61 69 Spot42 48 56 -9.48 0.0203245 0.9238006 ddpA DD-dipeptide ABC transporter periplasmic binding protein
b2622 62 69 Spot42 49 56 -9.01 0.0264814 0.9238006 intA CP4-57 prophage integrase
b1182 60 69 Spot42 20 29 -8.85 0.028969 0.9238006 hlyE hemolysin E
b0307 57 71 Spot42 48 60 -10.37 0.0122776 0.9238006 ykgF ferridoxin-like LutB family protein putative electron transport chain YkgEFG component
b1867 51 72 Spot42 5 25 -9.93 0.0157589 0.9238006 yecD isochorismatase family protein
b1563 62 72 Spot42 44 55 -9.07 0.0256036 0.9238006 relE Qin prophage toxin of the RelE-RelB toxin-antitoxin system
b1596 63 73 Spot42 56 66 -10.86 0.0092897 0.9238006 ynfM putative arabinose efflux transporter
b0878 64 73 Spot42 47 56 -9.01 0.0264814 0.9238006 macA macrolide transporter membrane fusion protein (MFP) component
b0062 67 73 Spot42 1 7 -8.79 0.0299597 0.9238006 araA L-arabinose isomerase
b3354 58 73 Spot42 43 57 -8.76 0.0304675 0.9238006 yheU UPF0270 family protein
b2935 63 75 Spot42 52 64 -12.34 0.003983 0.9238006 tktA transketolase 1 thiamine triphosphate-binding
b0973 67 75 Spot42 48 56 -11.79 0.0054601 0.9238006 hyaB hydrogenase 1 large subunit
b1921 60 75 Spot42 49 65 -9.65 0.0184641 0.9238006 fliZ RpoS antagonist putative regulator of FliA activity
b1056 68 75 Spot42 49 56 -9.26 0.023008 0.9238006 yceI periplasmic high pH-inducible lipid-binding protein
b2619 67 75 Spot42 1 9 -8.94 0.0275429 0.9238006 ratA toxic UPF0083 family protein inhibitor of 70S ribosome formation
Rows: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 all

Details of Selected Interaction Download Interaction Details

Target

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Results are computed with IntaRNA version 3.1.3 linking Vienna RNA package 2.4.14